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New Plasmodium vivax Genomes From the China-Myanmar Border
Plasmodium vivax is increasingly the dominant species of malaria in the Greater Mekong Subregion (GMS), which is pursuing regional malaria elimination. P. vivax lineages in the GMS are poorly characterized. Currently, P. vivax reference genomes are scarce due to difficulties in culturing the parasit...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7432439/ https://www.ncbi.nlm.nih.gov/pubmed/32849480 http://dx.doi.org/10.3389/fmicb.2020.01930 |
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author | Brashear, Awtum M. Huckaby, Adam C. Fan, Qi Dillard, Luke J. Hu, Yubing Li, Yuling Zhao, Yan Wang, Zenglei Cao, Yaming Miao, Jun Guler, Jennifer L. Cui, Liwang |
author_facet | Brashear, Awtum M. Huckaby, Adam C. Fan, Qi Dillard, Luke J. Hu, Yubing Li, Yuling Zhao, Yan Wang, Zenglei Cao, Yaming Miao, Jun Guler, Jennifer L. Cui, Liwang |
author_sort | Brashear, Awtum M. |
collection | PubMed |
description | Plasmodium vivax is increasingly the dominant species of malaria in the Greater Mekong Subregion (GMS), which is pursuing regional malaria elimination. P. vivax lineages in the GMS are poorly characterized. Currently, P. vivax reference genomes are scarce due to difficulties in culturing the parasite and lack of high-quality samples. In addition, P. vivax is incredibly diverse, necessitating the procurement of reference genomes from different geographical regions. Here we present four new P. vivax draft genomes assembled de novo from clinical samples collected in the China-Myanmar border area. We demonstrate comparable length and content to existing genomes, with the majority of structural variation occurring around subtelomeric regions and exported proteins, which we corroborated with detection of copy number variations in these regions. We predicted peptides from all PIR gene subfamilies, except for PIR D. We confirmed that proteins classically labeled as PIR D family members are not identifiable by PIR motifs, and actually bear stronger resemblance to DUF (domain of unknown function) family DUF3671, potentially pointing to a new, closely related gene family. Further, phylogenetic analyses of MSP7 genes showed high variability within the MSP7-B family compared to MSP7-A and -C families, and the result was comparable to that from whole genome analyses. The new genome assemblies serve as a resource for studying P. vivax within the GMS. |
format | Online Article Text |
id | pubmed-7432439 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-74324392020-08-25 New Plasmodium vivax Genomes From the China-Myanmar Border Brashear, Awtum M. Huckaby, Adam C. Fan, Qi Dillard, Luke J. Hu, Yubing Li, Yuling Zhao, Yan Wang, Zenglei Cao, Yaming Miao, Jun Guler, Jennifer L. Cui, Liwang Front Microbiol Microbiology Plasmodium vivax is increasingly the dominant species of malaria in the Greater Mekong Subregion (GMS), which is pursuing regional malaria elimination. P. vivax lineages in the GMS are poorly characterized. Currently, P. vivax reference genomes are scarce due to difficulties in culturing the parasite and lack of high-quality samples. In addition, P. vivax is incredibly diverse, necessitating the procurement of reference genomes from different geographical regions. Here we present four new P. vivax draft genomes assembled de novo from clinical samples collected in the China-Myanmar border area. We demonstrate comparable length and content to existing genomes, with the majority of structural variation occurring around subtelomeric regions and exported proteins, which we corroborated with detection of copy number variations in these regions. We predicted peptides from all PIR gene subfamilies, except for PIR D. We confirmed that proteins classically labeled as PIR D family members are not identifiable by PIR motifs, and actually bear stronger resemblance to DUF (domain of unknown function) family DUF3671, potentially pointing to a new, closely related gene family. Further, phylogenetic analyses of MSP7 genes showed high variability within the MSP7-B family compared to MSP7-A and -C families, and the result was comparable to that from whole genome analyses. The new genome assemblies serve as a resource for studying P. vivax within the GMS. Frontiers Media S.A. 2020-08-11 /pmc/articles/PMC7432439/ /pubmed/32849480 http://dx.doi.org/10.3389/fmicb.2020.01930 Text en Copyright © 2020 Brashear, Huckaby, Fan, Dillard, Hu, Li, Zhao, Wang, Cao, Miao, Guler and Cui. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Brashear, Awtum M. Huckaby, Adam C. Fan, Qi Dillard, Luke J. Hu, Yubing Li, Yuling Zhao, Yan Wang, Zenglei Cao, Yaming Miao, Jun Guler, Jennifer L. Cui, Liwang New Plasmodium vivax Genomes From the China-Myanmar Border |
title | New Plasmodium vivax Genomes From the China-Myanmar Border |
title_full | New Plasmodium vivax Genomes From the China-Myanmar Border |
title_fullStr | New Plasmodium vivax Genomes From the China-Myanmar Border |
title_full_unstemmed | New Plasmodium vivax Genomes From the China-Myanmar Border |
title_short | New Plasmodium vivax Genomes From the China-Myanmar Border |
title_sort | new plasmodium vivax genomes from the china-myanmar border |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7432439/ https://www.ncbi.nlm.nih.gov/pubmed/32849480 http://dx.doi.org/10.3389/fmicb.2020.01930 |
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